Hi,

I'm sorry if this this question is probably basic and statistically related.

I am analyzing 24 affy slides taken from GEO, 12 slides for each of the two
conditions.  According to the limma vignetetts chapter 8.5, I can have kinds
of two design matrix. What are the differences?

So I can either do "treatment-contrasts parameterization":
    design <- cbind(NORMAL=1, NORMALvsCANCER=c(rep(0, times=12), rep(1,
times=12)))
or linear contrasts:
    design <- cbind(NORMAL=c(rep(1, times=12), rep(0, times=12)),
                           CANCER=c(rep(0, times=12), rep(1, times=12)))

I am not sure which to choose, I currently uses the second method.

Timothy

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